In [1]:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# LEARN FCN00
#
from __future__ import print_function
import argparse
import os
import numpy as np
import pickle
from keras import backend as K
from keras.callbacks import ModelCheckpoint
from keras.models import Model
from keras.layers import Input
from keras.layers import Conv2D, MaxPooling2D, UpSampling2D, Concatenate, AveragePooling2D
from keras.layers import merge
from keras.optimizers import Adam, SGD, RMSprop
from keras.preprocessing.image import list_pictures, array_to_img
from image_ext import list_pictures_in_multidir, load_imgs_asarray, img_dice_coeff
# MAXPOOLING
#from create_fcn import create_fcn01, create_fcn02, create_fcn00
# AVERAGE POOLING
from create_fcn_avpool import create_fcn01,create_fcn00
np.random.seed(2016)
In [2]:
def dice_coef(y_true, y_pred):
y_true = K.flatten(y_true)
y_pred = K.flatten(y_pred)
intersection = K.sum(y_true * y_pred)
return (2.*intersection + 1) / (K.sum(y_true) + K.sum(y_pred) + 1)
def dice_coef_loss(y_true, y_pred):
return -dice_coef(y_true, y_pred)
In [3]:
def load_fnames(paths):
f = open(paths)
data1 = f.read()
f.close()
lines = data1.split('\n')
#print(len(lines))
# 最終行は空行なので消す
del(lines[len(lines)-1])
#print(len(lines))
return lines
In [4]:
def make_fnames(fnames,fpath,fpath_mask,mask_ext):
fnames_img = [];
fnames_mask= [];
for i in range(len(fnames)):
fnames_img.append(fpath + '/' + fnames[i]);
fnames_mask.append(fpath_mask + '/' + mask_ext + fnames[i]);
return [fnames_img,fnames_mask]
In [5]:
#
# MAIN STARTS FROM HERE
#
if __name__ == '__main__':
target_size = (224, 224)
dpath_this = './'
dname_checkpoints = 'checkpoints_fcn00_avpool.augumented'
dname_checkpoints_fcn01 = 'checkpoints_fcn01_avpool'
dname_outputs = 'outputs'
fname_architecture = 'architecture.json'
fname_weights = "model_weights_{epoch:02d}.h5"
fname_stats = 'stats01.npz'
dim_ordering = 'channels_first'
fname_history = "history.pkl"
# definision of mode, LEARN or TEST or SHOW_HISTORY
#mode = "LEARN"
#mode = "SHOW_HISTORY"
#mode = "TEST"
# モデルを作成
print('creating model fcn00 and fcn01...')
#model_fcn02 = create_fcn02(target_size)
model_fcn01 = create_fcn01(target_size)
model_fcn00 = create_fcn00(target_size)
if os.path.exists(dname_checkpoints) == 0:
os.mkdir(dname_checkpoints)
In [6]:
#
# LEARNING MODE
#
mode = "LEARN"
if mode == "LEARN":
# Read Learning Data
# fnames = load_fnames('data/list_train_01.txt')
# [fpaths_xs_train,fpaths_ys_train] = make_fnames(fnames,'data/img','data/mask','OperatorA_')
# fnames = load_fnames('data.nnlab/list_train_01.txt')
# fnames = load_fnames('data/list_train_01.txt')
fnames = load_fnames('data_augumented/list_train_01.txt')
# [fpaths_xs_train,fpaths_ys_train] = make_fnames(fnames,'data.nnlab/image','data.nnlab/gt','')
[fpaths_xs_train,fpaths_ys_train] = make_fnames(fnames,'data_augumented/img','data_augumented/mask','')
print('reading training data')
X_train = load_imgs_asarray(fpaths_xs_train, grayscale=False, target_size=target_size,
dim_ordering=dim_ordering)
print('reading traking gt data')
Y_train = load_imgs_asarray(fpaths_ys_train, grayscale=True, target_size=target_size,
dim_ordering=dim_ordering)
# Read Validation Data
# fnames = load_fnames('data/list_valid_01.txt')
# [fpaths_xs_valid,fpaths_ys_valid] = make_fnames(fnames,'data/img','data/mask','OperatorA_')
fnames = load_fnames('data_augumented/list_valid_01.txt')
[fpaths_xs_valid,fpaths_ys_valid] = make_fnames(fnames,'data_augumented/img','data_augumented/mask','')
print('reading validation data')
X_valid = load_imgs_asarray(fpaths_xs_valid, grayscale=False, target_size=target_size,
dim_ordering=dim_ordering)
Y_valid = load_imgs_asarray(fpaths_ys_valid, grayscale=True, target_size=target_size,
dim_ordering=dim_ordering)
print('==> ' + str(len(X_train)) + ' training images loaded')
print('==> ' + str(len(Y_train)) + ' training masks loaded')
print('==> ' + str(len(X_valid)) + ' validation images loaded')
print('==> ' + str(len(Y_valid)) + ' validation masks loaded')
# 前処理
print('computing mean and standard deviation...')
mean = np.mean(X_train, axis=(0, 2, 3))
std = np.std(X_train, axis=(0, 2, 3))
print('==> mean: ' + str(mean))
print('==> std : ' + str(std))
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print('saving mean and standard deviation to ' + fname_stats + '...')
stats = {'mean': mean, 'std': std}
np.savez(dname_checkpoints + '/' + fname_stats, **stats)
print('==> done')
print('globally normalizing data...')
for i in range(3):
X_train[:, i] = (X_train[:, i] - mean[i]) / std[i]
X_valid[:, i] = (X_valid[:, i] - mean[i]) / std[i]
Y_train /= 255
Y_valid /= 255
print('==> done')
In [8]:
init_from_fcn01 = 0
if init_from_fcn01 == 1:
# モデルに学習済のfcn01 Weightをロードする
epoch = 100
fname_weights = 'model_weights_%02d.h5'%(epoch)
fpath_weights_fcn01 = os.path.join(dname_checkpoints_fcn01, fname_weights)
model_fcn01.load_weights(fpath_weights_fcn01)
#print('==> done')
# load weights from Learned U-NET
layer_names = ['conv1_1','conv1_2','conv2_1','conv2_2','conv3_1','conv3_2',
'conv4_1','conv4_2','conv5_1', 'conv5_2',
'up1_1', 'up1_2', 'up2_1', 'up2_2', 'up3_1', 'up3_2', 'up4_1',
'up4_2', 'conv_fin']
layer_names = ['conv1_1','conv1_2','conv2_1','conv2_2',
'up1_1', 'up1_2', 'up2_1', 'up2_2', 'conv_fin']
print('copying layer weights')
for name in layer_names:
print(name)
model_fcn00.get_layer(name).set_weights(model_fcn01.get_layer(name).get_weights())
model_fcn00.get_layer(name).trainable = True
In [9]:
# 損失関数，最適化手法を定義
adam = Adam(lr=1e-5)
sgd = SGD(lr=1e-3, decay=1e-6, momentum=0.95, nesterov=True)
#rmsprop = RMSprop(lr=0.001, rho=0.9, epsilon=1e-08, decay=0.0)
model_fcn00.compile(optimizer=adam, loss=dice_coef_loss, metrics=[dice_coef])
# 構造・重みを保存するディレクトリーの有無を確認
dpath_checkpoints = os.path.join(dpath_this, dname_checkpoints)
if not os.path.isdir(dpath_checkpoints):
os.mkdir(dpath_checkpoints)
# 重みを保存するためのオブジェクトを用意
fname_weights = "model_weights_{epoch:02d}.h5"
fpath_weights = os.path.join(dpath_checkpoints, fname_weights)
checkpointer = ModelCheckpoint(filepath=fpath_weights, save_best_only=False)
In [10]:
# トレーニングを開始
print('start training...')
history = model_fcn00.fit(X_train[:,:,:,:], Y_train[:,:,:,:], batch_size=64, epochs=200, verbose=1,
shuffle=True, validation_data=(X_valid, Y_valid), callbacks=[checkpointer])
In [11]:
# Save History
f = open(dname_checkpoints + '/' + fname_history,'wb')
pickle.dump(history.history,f)
f.close
Out[11]:
In [14]:
#
# TEST MODE
#
mode = 'TEST'
if mode == "TEST":
# Prediction (test) mode
# Read Test Data
fnames = load_fnames('data/list_test_01.txt')
#fnames = load_fnames('data.nnlab/list_test_01.txt')
[fpaths_xs_test,fpaths_ys_test] = make_fnames(fnames,'data/img','data/mask','OperatorA_')
#[fpaths_xs_test,fpaths_ys_test] = make_fnames(fnames,'data.nnlab/image','data.nnlab/gt','')
X_test = load_imgs_asarray(fpaths_xs_test, grayscale=False, target_size=target_size,
dim_ordering=dim_ordering)
Y_test = load_imgs_asarray(fpaths_ys_test, grayscale=True, target_size=target_size,
dim_ordering=dim_ordering)
# トレーニング時に計算した平均・標準偏差をロード
print('loading mean and standard deviation from ' + fname_stats + '...')
stats = np.load(dname_checkpoints + '/' + fname_stats)
mean = stats['mean']
std = stats['std']
print('==> mean: ' + str(mean))
print('==> std : ' + str(std))
for i in range(3):
X_test[:, i] = (X_test[:, i] - mean[i]) / std[i]
print('==> done')
In [15]:
from PIL import Image
import matplotlib.pyplot as plt
# 学習済みの重みをロード
epoch = 100
fname_weights = 'model_weights_%02d.h5'%(epoch)
fpath_weights = os.path.join(dname_checkpoints, fname_weights)
model_fcn00.load_weights(fpath_weights)
print('==> done')
# テストを開始
outputs = model_fcn00.predict(X_test)
# outputs = model_fcn02.predict(X_test)
# 出力を画像として保存
dname_outputs = './outputs/'
if not os.path.isdir(dname_outputs):
print('create directory: %s'%(dname_outputs))
os.mkdir(dname_outputs)
print('saving outputs as images...')
n = 0
for i, array in enumerate(outputs):
array = np.where(array > 0.5, 1, 0) # 二値に変換
array = array.astype(np.float32)
img_out = array_to_img(array, dim_ordering)
# fpath_out = os.path.join(dname_outputs, fnames[i])
fpath_out = os.path.join(dname_outputs, "%05d.png"%(n))
img_out.save(fpath_out)
n = n + 1
print('==> done')
n = 0
dice_eval = []
for i in range(len(fpaths_xs_test)):
# テスト画像
im1 = Image.open(fpaths_xs_test[i])
im1 = im1.resize((320,240))
# 出力結果
im2 = Image.open(os.path.join(dname_outputs, "%05d.png"%(n)))
im2 = im2.resize((320,240))
# Grond Truth
im3 = Image.open(fpaths_ys_test[i])
im3 = im3.resize((320,240))
im3 = im3.convert('L')
im2_d = np.zeros((240,320,3), 'uint8')
im2_d[:,:,0] = np.array(im2)
im2_d[:,:,1] = np.array(im3)*255
im2_d[:,:,2] = 0
# Compute dice coeff
im2a = np.array(im2)
im2a[im2a > 0] = 1
im3a = np.array(im3)
im3a[im3a > 0] = 1
overlap_a = np.array(im2a) * np.array(im3a)
overlap_b = np.array(im2a) + np.array(im3a)
#print('%03d: Dice Coeff = %f'%(i, 2*sum(sum(overlap_a))/sum(sum(overlap_b))))
#print('%f'%img_dice_coeff(im2,im3))
dice_eval.append(2*sum(sum(overlap_a))/sum(sum(overlap_b)))
print('%d: Dice eval : %f'%(n,2*sum(sum(overlap_a))/sum(sum(overlap_b))))
plt.imshow(np.hstack((np.array(im1),np.array(im2_d))))
plt.show()
n = n + 1
print('%d: Dice eval av. : %f'%(epoch,np.mean(np.array(dice_eval))))
In [19]:
#
# Show History
#
mode = "SHOW_HISTORY"
if mode == "SHOW_HISTORY":
# load pickle
print(dname_checkpoints + '/' + fname_history)
history = pickle.load(open(dname_checkpoints + '/' + fname_history, 'rb'))
for k in history.keys():
plt.plot(history[k])
plt.title(k)
plt.show()
